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FASIMU specifications


Unique identifier OMICS_05179
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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FASIMU citations


Model driven discovery of long chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells

PLoS Comput Biol
PMCID: 5766231
PMID: 29293497
DOI: 10.1371/journal.pcbi.1005914

[…] blocked reactions from the model. these reactions are those incapable of carrying any metabolic flux in steady state []. to this aim we first performed a flux variability analysis (fva) [–] using fasimu software []. this analysis computes minimal and maximal flux in each reaction. each analysis evaluates the feasibility of the simulation. the reactions in which their maximization […]


Improving Collaboration by Standardization Efforts in Systems Biology

Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] model building and simulation, which can calculate steady-state solutions for complex enzyme reactions and even solve ode and dae systems with delays and events. further important tools for fba are fasimu (hoppe et al., ), the vanted (junker et al., ) plug-in fba-simvis (grafahrend-belau et al., ), and pysces (olivier et al., )., the main focus of the mass-toolbox (palsson, ; sonnenschein […]


Precise generation of systems biology models from KEGG pathways

BMC Syst Biol
PMCID: 3623889
PMID: 23433509
DOI: 10.1186/1752-0509-7-15

[…] []. these formats can be used with graphical modeling applications (e.g., celldesigner [] or cytoscape []), complemented with rate laws (e.g., sbmlsqueezer []), used for flux balance analysis (e.g., fasimu []), and many more applications. therefore, converters exist that perform mostly basic conversions from kgml to those formats [-]. the drawback of many of those converters is that even […]


Metabolic Consequences of TGFβ Stimulation in Cultured Primary Mouse Hepatocytes Screened from Transcript Data with ModeScore

PMCID: 3901234
PMID: 24957771
DOI: 10.3390/metabo2040983

[…] c/t 24 h comparisons). , metabolism is represented by a modified version of hepatonet1 [] (see and ) and 987 reference functions (see and ) for which flux distributions have been computed using fasimu [], see . in the modescore method ([], see also ) a regulation amplitude for each reference flux distribution and each pair of transcript profiles is computed. this value is compatible […]


What mRNA Abundances Can Tell us about Metabolism

PMCID: 3901220
PMID: 24957650
DOI: 10.3390/metabo2030614

[…] the input/output fluxes [,] or directly in the flux-balance optimization []. , these expression-based prediction methods have been implemented in the universal flux computation frameworks cobra [] and fasimu []. for the imat method [] a standalone implementation is available []. the software for quantitative application of transcript data for flux prediction by lee et al. is also freely available […]

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FASIMU institution(s)
Institute of Biochemistry, University Medicine Charité Berlin, Berlin, Germany

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